4MFE

Structure of the carboxyl transferase domain from Rhizobium etli pyruvate carboxylase with 3-hydroxypyruvate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4JX4PDB ENTRY 4JX4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH CRYSTALLIZATION UNDER OIL629811.3% (w/v) PEG 8000, 99 mM BisTris, 346 mM tetramethylammonium chloride, pH 6.0, BATCH CRYSTALLIZATION UNDER OIL, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8957.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.254α = 90
b = 157.849β = 90
c = 243.319γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.979APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.650960.06622.85.59580791812-359.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.6493.20.4343.35.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4JX42.6149.3790882479795.670.179490.177120.22463RANDOM74.213
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
4.55-0.99-3.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.087
r_dihedral_angle_4_deg20.104
r_dihedral_angle_3_deg15.222
r_dihedral_angle_1_deg6.373
r_long_range_B_refined6.27
r_long_range_B_other6.27
r_scangle_other3.763
r_mcangle_it3.613
r_mcangle_other3.613
r_scbond_it2.954
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.087
r_dihedral_angle_4_deg20.104
r_dihedral_angle_3_deg15.222
r_dihedral_angle_1_deg6.373
r_long_range_B_refined6.27
r_long_range_B_other6.27
r_scangle_other3.763
r_mcangle_it3.613
r_mcangle_other3.613
r_scbond_it2.954
r_scbond_other2.954
r_mcbond_it2.4
r_mcbond_other2.4
r_angle_refined_deg1.727
r_angle_other_deg0.878
r_chiral_restr0.088
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17458
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms89

Software

Software
Software NamePurpose
MD2data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling